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RcsB-BglJ DNA-binding transcriptional activator

Synonyms: RcsB-BglJ
Summary:
RcsB-BglJ is a pleiotropic transcriptional activator that coordinates regulation with global regulators, including CRP, LeuO, and HNS. BglJ-RcsB is active independently of RcsB phosphorylation [1, 4, 5] Regulation by heteromeric transcription factors is a rare event in the bacterial word [4] A 20-bp consensus sequence motif has been proposed for RcsB-BglJ based on analysis with the MEME suite [4] RcsB-BglJ acts antagonistically as well as synergistically with additional transcription factors, such as HNS, CRP, and LeuO. Activation by RcsB-BglJ occurs both at non-HNS-repressed promoters as well as at promoters repressed by HNS and/or StpA [4]


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RcsB-BglJ Functional   [APPHINH], [IEP], [IFC], [IMP], [IPI] [1]
Connectivity class: Local Regulator
Gene name: bglJ
  Genome position: 4604160-4604837
  Length: 678 bp / 225 aa
Operon name: yjjQ-bglJ
TU(s) encoding the TF:
Transcription unit        Promoter
yjjQ-bglJ
yjjQp
Gene name: rcsB
  Genome position: 2316177-2316827
  Length: 651 bp / 216 aa
Operon name: rcsDB
TU(s) encoding the TF:
Transcription unit        Promoter
rcsB
rcsBp1
rcsB
rcsBp2
rcsDB
rcsDp


Regulon       
Regulated gene(s) bglB, bglF, bglG, leuO, sfsB, yecT, yehF, ygiZ, yidL, ykiA, ynbA, ynbB, ynbC, ynbD, ynjI, yqhG
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (4)
Transcription related (4)
activator (4)
operon (2)
posttranslational modification (1)
Read more >
Regulated operon(s) bglGFB, leuO, sfsB, yecT, yehF, ygiZ, yidL, ykiA, ynbABCD, ynjI, yqhG
First gene in the operon(s) bglG, leuO, sfsB, yecT, yehF, ygiZ, yidL, ykiA, ynbA, ynjI, yqhG
Simple and complex regulons CRP,Fis,H-NS,LeuO,RcsB-BglJ,StpA
CRP,RcsB-BglJ
H-NS,LeuO,RcsB-BglJ,StpA
LexA,RcsB-BglJ
RcsB-BglJ
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[RcsB-BglJ,+](12)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
 LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  RcsB-BglJ activator bglGp nd -95.5 -225.5 bglG, bglF, bglB
ttatatataaCTTTATAAATTCCTAAAATTacacaaagtt
 3906783 3906802 [AIBSCS], [APIORCISFBSCS], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [1], [2], [3], [4]
  RcsB-BglJ activator bglGp2 nd -75.5 -225.5 bglG
ttatatataaCTTTATAAATTCCTAAAATTacacaaagtt
 3906783 3906802 [AIBSCS], [APIORCISFBSCS], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [1], [2], [3], [4]
  RcsB-BglJ activator leuOp2 nd -58.5 -122.5 leuO
cagaacccgtATCTTTATGTTTTCCGAATTttactcattt
 84236 84255 [APIORCISFBSCS], [CV(CHIP-SV/GEA/ROMA)], [CV(CHIP-SV/SM)], [CV(GEA/ROMA)], [CV(GEA/ROMA/SM)], [GEA], [SM] [5]
  RcsB-BglJ activator sfsBp nd -67.5 -118.5 sfsB
ggatgtgcatCTTTATATATTCTGAATATTCacactcttta
 3334781 3334801 [AIBSCS], [CV(GEA/ROMA)], [GEA] [4]
  RcsB-BglJ activator yecTp nd -68.5 -105.5 yecT
ttattgccatCTAAATGTATTCTGAAAATGGacatgccatt
 1961857 1961877 [AIBSCS], [CV(GEA/ROMA)], [GEA] [4]
  RcsB-BglJ activator yehFp Sigma70 -66.5 -95.5 yehF
agcgccttttCTTTATAAATTCCTAAAGTTGttttcttgcg
 2196369 2196389 [AIBSCS], [CV(GEA/ROMA)], [GEA] [4]
  RcsB-BglJ activator ygiZp nd -65.5 -177.5 ygiZ
accgatgcagGATAAATATTTTCTGAAAATGacaatactga
 3172379 3172399 [AIBSCS], [CV(GEA/ROMA)], [GEA] [4]
  RcsB-BglJ activator yidLp nd -51.5 -81.5 yidL
gtcaggcagtCAGATTCTTAAAATACAAACGtcgtatccct
 3860192 3860212 [AIBSCS], [CV(GEA/ROMA)], [GEA] [4]
  RcsB-BglJ activator ykiAp nd -78.5 -113.5 ykiA
cttgaacgggAGGGCATTTTTCTGAAATATCctttctttag
 408486 408506 [AIBSCS], [CV(GEA/ROMA)], [GEA] [4]
  RcsB-BglJ activator ynbAp nd -65.5 -89.5 ynbA, ynbB, ynbC, ynbD
tccccaatacCTTGATATATTCTGAATTTTTaatgaaacgg
 1477522 1477542 [AIBSCS], [CV(GEA/ROMA)], [GEA] [4]
  RcsB-BglJ activator ynjIp nd -65.5 -94.5 ynjI
ttcgtgctatTCGAGTCATATTCTGAAATATccagcggatc
 1844956 1844976 [AIBSCS], [CV(GEA/ROMA)], [GEA] [4]
  RcsB-BglJ activator yqhGp nd -44.5 -149.5 yqhG
ccgctaccggACTTTTCAGAAATCATTTATTcccctcgcgt
 3157491 3157511 [AIBSCS], [CV(GEA/ROMA)], [GEA] [4]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [APPHINH] Assay of protein purified to homogeneity from its native host

 [IEP] Inferred from expression pattern

 [IFC] Inferred by functional complementation

 [IMP] Inferred from mutant phenotype

 [IPI] Inferred from physical interaction

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [CV(CHIP-SV/GEA/ROMA)] cross validation(CHIP-SV/GEA/ROMA)

 [CV(CHIP-SV/SM)] cross validation(CHIP-SV/SM)

 [CV(GEA/ROMA)] cross validation(GEA/ROMA)

 [CV(GEA/ROMA/SM)] cross validation(GEA/ROMA/SM)

 [GEA] Gene expression analysis

 [SM] Site mutation


Reference(s)    

 [1] Venkatesh GR., Kembou Koungni FC., Paukner A., Stratmann T., Blissenbach B., Schnetz K., 2010, BglJ-RcsB heterodimers relieve repression of the Escherichia coli bgl operon by H-NS., J Bacteriol 192(24):6456-64

 [2] Giel M., Desnoyer M., Lopilato J., 1996, A mutation in a new gene, bglJ, activates the bgl operon in Escherichia coli K-12., Genetics 143(2):627-35

 [3] Madhusudan S., Paukner A., Klingen Y., Schnetz K., 2005, Independent regulation of H-NS-mediated silencing of the bgl operon at two levels: upstream by BglJ and LeuO and downstream by DnaKJ., Microbiology 151(Pt 10):3349-59

 [4] Salscheider SL., Jahn A., Schnetz K., 2014, Transcriptional regulation by BglJ-RcsB, a pleiotropic heteromeric activator in Escherichia coli., Nucleic Acids Res 42(5):2999-3008

 [5] Stratmann T., Pul U., Wurm R., Wagner R., Schnetz K., 2012, RcsB-BglJ activates the Escherichia coli leuO gene, encoding an H-NS antagonist and pleiotropic regulator of virulence determinants., Mol Microbiol 83(6):1109-23


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